plotDistributions         package:arrayMagic         R Documentation

_V_i_s_u_a_l_i_s_e _D_i_s_t_r_i_b_u_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Boxplot like visualisation of distributions, only the boxes, i.e.
     the median and the second and third quartile are plotted (cf.
     'boxplot.stats' for the details on the calculation). The plots may
     help to identify shortcomings of the raw data or normalised data.
     The argument 'quantiles' can be used to visualize two or three
     arbitrary quantiles with boxes.

_U_s_a_g_e:

     plotDistributions(dataMatrix, transFunc, quantiles, main, labels, xlab, ylab, colourVector, width=8, height=6, fileName="plotDistributionsOutput", savePath, plotOutput="standard")

_A_r_g_u_m_e_n_t_s:

dataMatrix: numeric data matrix, where columns represent distributions,
          e.g. raw array data or normalised data; required; default
          missing

transFunc: unary function; optional; default missing. Data
          transformation function, e.g. log

quantiles: missing by default; a vector of two or three increasing
          quantiles used to determine the boxes to be drawn

    main: plot title; type character string; optional; default missing

  labels: vector of names, may substitute column names of 'dataMatrix';
          optional; default missing

    xlab: label for x axis; type character string; optional; default
          missing

    ylab: label for y axis; type character string; optional; default
          missing

colourVector: vector of colours; optional; default missing

   width: graphics window width; required; default: 8

  height: graphics window height; required; default: 6

fileName: optional; default: "plotDistributionsOutput"

savePath: optional; default: missing

plotOutput: character string specifying either "standard", "screen",
          "pdf", "win.metafile"; default: "standard"

_D_e_t_a_i_l_s:

     Default of 'transFunc' is no transformation, i.e. identity. If
     'labels' are supplied at first the column names or secondly a
     numbering  are used instead. By default the 'colourVector' is
     defined as alternating "darkred" and "darkgreen".

_V_a_l_u_e:

     The function is called for its side effect.

_A_u_t_h_o_r(_s):

     Andreas Buness <a.buness@dkfz.de>

_S_e_e _A_l_s_o:

     'boxplot.stats'

_E_x_a_m_p_l_e_s:

           plotDistributions(cbind(rnorm(100),rnorm(100)),
                  main="Random Gaussians", labels = c("N1","N2"), ylab="scale")
           plotDistributions(as.matrix(1:100), quantiles=c(0.25,0.85),
                  main = "Random Gaussians", labels = c("N1"), ylab = "scale")

